Mosquito Metagenomics Summary

Libraries

require(pacman)
pacman::p_load(tidyverse, janitor, here, DT, gt, phylotools, assertr, readxl, patchwork, reshape2, ggtext, openxlsx, grid, tiff)

Load Data

virus_master_2023 <- read_csv(here("Data/tblastx_master.csv"))

BLAST Summary

library_summary <- virus_master_2023 %>%
  group_by(mosquito_species, sample_number) %>%
  summarise(n = n_distinct(mosquito_species)) %>%
  group_by(mosquito_species) %>%
  summarise(n = n()) %>%
  adorn_totals()

years <- virus_master_2023 %>% 
  group_by(collection_year, virus_name) %>% 
  summarise(count = n_distinct(virus_name, collection_year)) %>% 
  pivot_wider(names_from = collection_year, values_from = count, values_fill = 0)

virus_lineage <- virus_master_2023 %>% 
  group_by(virus_name, viral_family, genome) %>% 
  summarise(n = n_distinct(virus_name, viral_family, genome)) %>% 
  select(-"n")

virus_master_2023 %>% 
  group_by(virus_name) %>% 
  summarise(n_contigs = n(),
            mean_cov = mean(coverage),
            min_cov = min(coverage),
            max_cov = max(coverage),
            mean_pid = mean(greatest_identity_percent),
            med_pid = median(greatest_identity_percent),
            min_pid = min(greatest_identity_percent),
            max_pid = max(greatest_identity_percent),
            total_reads = sum(total_read_count)) %>% 
  left_join(virus_lineage, by = "virus_name") %>% 
  group_by(genome, viral_family) %>% 
  arrange(genome, viral_family) %>% 
  relocate(total_reads, .after = "n_contigs") %>% 
  mutate(across(.cols = "virus_name",
                ~case_when(grepl("Manitoba", virus_name) & !grepl("Manitoba virus", virus_name) ~ 
                             paste0(., "*"),
                           TRUE ~ .))) %>% 
  gt() %>% 
  fmt_number(columns = mean_cov:max_pid,
             decimals = 2) %>% 
  fmt_number(columns = total_reads,
             sep_mark = ",",
             decimals = 0) %>% 
  tab_spanner(label = "Coverage Depth", columns = c(mean_cov, min_cov, max_cov)) %>% 
  tab_spanner(label = "aa Percent Identity", columns = c(mean_pid, min_pid, max_pid, med_pid)) %>% 
  cols_label(
    n_contigs = "Contigs",
    total_reads = "Reads",
    mean_cov = "Mean", min_cov = "Min", max_cov = "Max",
    mean_pid = "Mean", min_pid = "Min", max_pid = "Max", med_pid = "Median",
    virus_name = "Virus") %>% 
  tab_style(
    style = list(cell_fill(color = "grey"),
                 cell_text(weight = "bold")),
    locations = cells_row_groups(groups = everything())
  ) %>% 
  tab_style(
    style = cell_borders(
      sides = "left",
      weight = px(2),
      color = "grey"),
    locations = cells_body(
      columns = c(mean_cov, mean_pid, "n_contigs")
    )
  ) %>% 
  data_color(
    columns = mean_pid:max_pid,
    palette = "viridis"
    
  ) %>% 
  tab_footnote("* Putatively novel virus.")

Virus	Contigs	Reads	Coverage Depth			aa Percent Identity
			Mean	Min	Max	Mean	Min	Max	Median
+ssRNA - Dicistroviridae
Black queen cell virus	2	1,613	17.00	11.15	22.85	100.00	100.00	100.00	100.00
Manitoba dicistro-like virus 1*	1	10,688	149.27	149.27	149.27	82.61	82.61	82.61	82.61
Soybean thrips dicistrovirus	11	11,192	17.32	10.11	29.01	100.00	100.00	100.00	100.00
+ssRNA - Flaviviridae
Inari jingmenvirus	1	139	11.02	11.02	11.02	100.00	100.00	100.00	100.00
Placeda virus	169	106,682	90.37	10.02	1,114.82	97.87	86.24	100.00	98.55
+ssRNA - Iflaviridae
Cafluga virus	2	976	20.82	19.41	22.24	99.77	99.55	100.00	99.77
Culex Iflavi-like virus 4	23	13,815	22.81	10.65	58.90	99.81	96.20	100.00	100.00
Culex iflavilike virus 3	183	266,451	284.65	18.65	1,269.06	99.49	94.19	100.00	100.00
Hanko iflavirus 1	30	2,938,402	3,394.01	10.99	19,795.35	97.49	93.45	100.00	97.30
Hanko iflavirus 2	29	29,456	86.71	16.30	242.52	88.70	67.08	100.00	89.58
Hubei arthropod virus 1	1	352	11.95	11.95	11.95	100.00	100.00	100.00	100.00
Manitoba iflavirus 1*	25	39,865	28.41	10.35	266.71	93.47	89.14	100.00	93.38
Manitoba picorna-like virus 1*	86	72,405	64.99	10.27	207.10	87.73	73.93	100.00	87.80
Soybean thrips iflavirus 4	1	636	16.60	16.60	16.60	100.00	100.00	100.00	100.00
Yongsan picorna-like virus 2	4	58,132	165.26	34.98	535.91	100.00	100.00	100.00	100.00
+ssRNA - Luteoviridae
Marma virus	23	39,344	70.95	11.62	129.64	100.00	100.00	100.00	100.00
+ssRNA - Narnaviridae
Culex narnavirus 1	1	63	12.07	12.07	12.07	100.00	100.00	100.00	100.00
Manitoba narnavirus 1*	2	391	18.77	13.02	24.52	80.59	80.29	80.89	80.59
+ssRNA - Negevirus
Cordoba virus	14	135,594	548.17	17.51	2,225.85	97.10	93.75	100.00	97.23
Manitoba mononega-like virus 1*	3	12,701	45.19	33.85	59.07	80.60	73.21	90.00	78.57
Manitoba mononega-like virus 2*	3	6,079	37.12	18.89	65.64	98.77	96.30	100.00	100.00
Mekrijarvi Negevirus	6	167,549	294.01	30.28	1,262.63	94.13	90.78	100.00	93.40
Serbia mononega-like virus 1	1	494	20.03	20.03	20.03	75.00	75.00	75.00	75.00
Utsjoki negevirus 3	2	416	21.12	18.00	24.24	99.02	99.01	99.03	99.02
+ssRNA - Nodaviridae
Hubei noda-like virus 12	2	4,244	54.47	23.60	85.34	95.83	91.67	100.00	95.83
+ssRNA - Rhabdoviridae
Manitoba Rhabdovirus 1*	37	32,534	34.99	10.21	120.41	83.22	69.42	93.01	83.33
+ssRNA - Tombusviridae
Des Moines River virus	4	35,117	486.06	34.94	897.17	100.00	100.00	100.00	100.00
Hubei mosquito virus 4	6	2,919	16.68	10.02	39.59	96.50	92.65	100.00	95.70
Manitoba tombus-like virus 1*	6	28,922	224.21	74.52	557.41	79.73	72.73	100.00	76.56
+ssRNA - Tymoviridae
Hubei macula-like virus 3	8	530,385	1,092.52	11.15	7,749.86	96.13	92.15	100.00	96.63
Manitoba tymo-like virus 1*	1	1,482	23.67	23.67	23.67	66.79	66.79	66.79	66.79
+ssRNA - Virgaviridae
Hubei virga-like virus 2	6	505	13.26	10.94	15.50	99.04	96.27	100.00	100.00
Manitoba virgavirus 1*	1	186	11.06	11.06	11.06	83.83	83.83	83.83	83.83
-ssRNA - Chuviridae
Chuvirus	39	22,130	28.00	10.17	214.52	97.49	89.66	100.00	97.02
-ssRNA - Culex rhabdovirus
Culex rhabdovirus	2	997	116.26	74.47	158.06	100.00	100.00	100.00	100.00
-ssRNA - Flanders hapavirus
Flanders hapavirus	81	104,235	113.05	10.00	686.87	99.90	95.96	100.00	100.00
-ssRNA - Orthomyxoviridae
Astopletus virus	29	5,975	32.63	10.91	107.95	99.06	95.77	100.00	100.00
Wuhan mosquito virus 6	101	133,667	176.35	12.58	641.58	99.76	97.69	100.00	100.00
-ssRNA - Peribunyaviridae
Culex bunyavirus 2	19	6,255	23.92	10.28	49.84	100.00	100.00	100.00	100.00
-ssRNA - Rhabdoviridae
Canya virus	14	3,766	24.71	11.30	66.33	87.32	66.04	100.00	85.07
Culex Rhabdo-like virus	4	807	14.68	10.87	23.28	100.00	100.00	100.00	100.00
Elisy virus	21	3,849	19.29	10.10	40.69	99.27	96.41	100.00	100.00
Manitoba rhabdovirus 2*	1	2,401	51.70	51.70	51.70	75.00	75.00	75.00	75.00
Manitoba virus	5	1,003	19.71	15.74	24.80	99.76	98.80	100.00	100.00
Merida virus	55	76,697	91.60	11.06	276.87	99.86	97.14	100.00	100.00
dsDNA - Iridoviridae
Manitoba iridescent virus 1*	1	137	16.99	16.99	16.99	78.74	78.74	78.74	78.74
dsRNA - Birnaviridae
Ballard Lake virus	48	682,541	431.81	10.84	2,260.59	99.86	93.27	100.00	100.00
dsRNA - Partitiviridae
Partitivirus-like Culex mosquito virus	12	4,477	23.28	11.49	45.83	100.00	100.00	100.00	100.00
dsRNA - Totiviridae
Gouley virus	3	117	12.22	10.42	14.89	95.04	92.86	97.67	94.59
Manitoba toti-like virus 1*	5	13,869	39.82	11.18	127.46	69.92	67.43	73.11	68.10
Manitoba toti-like virus 2*	1	418	13.45	13.45	13.45	60.24	60.24	60.24	60.24
Manitoba toti-like virus 3*	4	1,772	15.11	11.20	18.40	73.53	72.22	74.90	73.50
Manitoba toti-like virus 4*	1	702	14.41	14.41	14.41	89.07	89.07	89.07	89.07
Snelk virus	4	496	41.15	23.15	67.61	100.00	100.00	100.00	100.00
ssDNA - Parvoviridae
Aedes albopictus densovirus	4	14,051	139.82	94.27	203.18	97.46	89.86	100.00	100.00
Aedes vexans densovirus isolate	1	594	17.69	17.69	17.69	100.00	100.00	100.00	100.00
Culex densovirus	8	6,035	127.22	11.65	490.03	99.56	97.71	100.00	100.00
MAG: Grus japonensis parvoviridae sp	1	366	60.82	60.82	60.82	100.00	100.00	100.00	100.00
* Putatively novel virus.

Virus Detections by Species

virus_master_2023 %>% 
  group_by(mosquito_species, virus_name) %>% 
  summarise(count = n_distinct(virus_name, sample_number)) %>% 
  pivot_wider(names_from = mosquito_species, values_from = count, values_fill = 0) %>% 
  mutate("Aedes canadensis \n Total: 1" = (`Aedes canadensis` / 1) * 100,
         "Aedes vexans \n Total: 19" = (`Aedes vexans` / 19) * 100,
         "Anopheles earlei \n Total: 1" = (`Anopheles earlei` / 1) * 100,
         "Coquillettidia perturbans \n Total: 6" = (`Coquillettidia perturbans` / 6) * 100,
         "Culex tarsalis \n Total: 11" = (`Culex tarsalis` / 11) * 100,
         "Ochlerotatus dorsalis \n Total: 5" = (`Ochlerotatus dorsalis` / 5) * 100,
         "Ochlerotatus flavescens \n Total: 1" = (`Ochlerotatus flavescens` / 1) * 100,
         "Ochlerotatus triseriatus \n Total: 1" = (`Ochlerotatus triseriatus` / 1) * 100,
  ) %>% select(-`Aedes canadensis`:-`Ochlerotatus triseriatus`) %>% 
  left_join(virus_lineage, by = "virus_name") %>% 
   left_join(years, by = "virus_name") %>% 
   relocate("2020", .after = "virus_name") %>% relocate("2021", .after = "2020") %>% 
   mutate(across(.cols = c("2020", "2021"),
                 ~case_when(. == "1" ~ TRUE,
                            . == "0" ~ FALSE))) %>% 
   mutate(across(.cols = "virus_name",
                 ~case_when(grepl("Manitoba", virus_name) & !grepl("Manitoba virus", virus_name) ~ 
                              paste0(., "*"),
                            TRUE ~ .))) %>% 
  group_by(genome, viral_family) %>% 
  arrange(genome, viral_family) %>% 
  gt() %>% 
  fmt_number(columns = "Aedes canadensis \n Total: 1":"Ochlerotatus triseriatus \n Total: 1",
             decimals = 2) %>% 
  tab_spanner(label = "Percent of Libraries Detected by Species", 
              columns = c("Aedes canadensis \n Total: 1":"Ochlerotatus triseriatus \n Total: 1")) %>% 
   tab_spanner(label = html("Years Detected"),
               columns = c("2020":"2021")) %>% 
  cols_label(
    "Aedes canadensis \n Total: 1" = html("<em>Aedes canadensis</em> <br> Total: 1"),
    "Aedes vexans \n Total: 19" = html("<em>Aedes vexans</em> <br> Total: 19"),
    "Anopheles earlei \n Total: 1" = html("<em>Anopheles earlei</em> <br> Total: 1"),
    "Coquillettidia perturbans \n Total: 6" = html("<em>Coquillettidia perturbans</em> <br> Total: 6"),
    "Culex tarsalis \n Total: 11" = html("<em>Culex tarsalis</em> <br> Total: 11"),
    "Ochlerotatus dorsalis \n Total: 5" = html("<em>Ochlerotatus dorsalis</em> <br> Total: 5"),
    "Ochlerotatus flavescens \n Total: 1" = html("<em>Ochlerotatus flavescens</em> <br> Total: 1"),
    "Ochlerotatus triseriatus \n Total: 1" = html("<em>Ochlerotatus triseriatus</em> <br> Total: 1"),
    virus_name = "Virus") %>% 
   cols_align(align = "center",
              columns = "2020":"Ochlerotatus triseriatus \n Total: 1") %>% 
   tab_style(
     style = list(cell_fill(color = "grey"),
                  cell_text(weight = "bold")),
     locations = cells_row_groups(groups = everything())) %>% 
   data_color(columns = `Aedes canadensis \n Total: 1`:last_col(),
              palette = "viridis", 
              direction = "row") %>% 
   tab_style(
     style = cell_borders(
       sides = "left",
       weight = px(2),
       color = "black"),
     locations = cells_body(
       columns = c("Aedes canadensis \n Total: 1"))) %>% 
  tab_footnote("* Putatively novel virus") %>% 
  tab_options(., container.width = 1500)

Virus	Years Detected		Percent of Libraries Detected by Species
	2020	2021	Aedes canadensis Total: 1	Aedes vexans Total: 19	Anopheles earlei Total: 1	Coquillettidia perturbans Total: 6	Culex tarsalis Total: 11	Ochlerotatus dorsalis Total: 5	Ochlerotatus flavescens Total: 1	Ochlerotatus triseriatus Total: 1
+ssRNA - Dicistroviridae
Black queen cell virus	TRUE	FALSE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Soybean thrips dicistrovirus	TRUE	TRUE	0.00	15.79	0.00	0.00	45.45	20.00	0.00	0.00
Manitoba dicistro-like virus 1*	TRUE	FALSE	0.00	0.00	0.00	0.00	9.09	0.00	0.00	0.00
+ssRNA - Flaviviridae
Inari jingmenvirus	TRUE	FALSE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Placeda virus	TRUE	TRUE	0.00	10.53	0.00	0.00	100.00	0.00	0.00	0.00
+ssRNA - Iflaviridae
Hanko iflavirus 1	TRUE	TRUE	0.00	21.05	0.00	16.67	9.09	100.00	100.00	0.00
Hanko iflavirus 2	TRUE	TRUE	0.00	78.95	0.00	16.67	0.00	40.00	0.00	0.00
Hubei arthropod virus 1	FALSE	TRUE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Manitoba iflavirus 1*	TRUE	TRUE	0.00	36.84	0.00	33.33	27.27	80.00	100.00	0.00
Manitoba picorna-like virus 1*	TRUE	TRUE	0.00	100.00	0.00	0.00	0.00	60.00	0.00	0.00
Cafluga virus	TRUE	FALSE	0.00	0.00	0.00	16.67	0.00	20.00	0.00	0.00
Soybean thrips iflavirus 4	TRUE	FALSE	0.00	0.00	0.00	16.67	0.00	0.00	0.00	0.00
Culex Iflavi-like virus 4	TRUE	TRUE	0.00	0.00	0.00	0.00	63.64	0.00	0.00	0.00
Culex iflavilike virus 3	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
Yongsan picorna-like virus 2	TRUE	TRUE	0.00	0.00	0.00	0.00	27.27	0.00	0.00	0.00
+ssRNA - Luteoviridae
Marma virus	TRUE	TRUE	0.00	0.00	0.00	16.67	100.00	0.00	0.00	0.00
+ssRNA - Narnaviridae
Manitoba narnavirus 1*	FALSE	TRUE	0.00	0.00	100.00	0.00	0.00	0.00	0.00	0.00
Culex narnavirus 1	TRUE	FALSE	0.00	0.00	0.00	0.00	9.09	0.00	0.00	0.00
+ssRNA - Negevirus
Manitoba mononega-like virus 1*	TRUE	TRUE	100.00	0.00	0.00	0.00	0.00	0.00	0.00	100.00
Serbia mononega-like virus 1	FALSE	TRUE	100.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
Cordoba virus	FALSE	TRUE	0.00	15.79	0.00	0.00	0.00	0.00	0.00	0.00
Manitoba mononega-like virus 2*	TRUE	TRUE	0.00	15.79	0.00	0.00	0.00	0.00	0.00	0.00
Mekrijarvi Negevirus	TRUE	TRUE	0.00	15.79	0.00	0.00	0.00	60.00	0.00	0.00
Utsjoki negevirus 3	TRUE	FALSE	0.00	10.53	0.00	0.00	0.00	0.00	0.00	0.00
+ssRNA - Nodaviridae
Hubei noda-like virus 12	FALSE	TRUE	0.00	0.00	0.00	16.67	9.09	0.00	0.00	0.00
+ssRNA - Rhabdoviridae
Manitoba Rhabdovirus 1*	TRUE	TRUE	0.00	100.00	0.00	0.00	0.00	20.00	0.00	0.00
+ssRNA - Tombusviridae
Des Moines River virus	TRUE	FALSE	0.00	5.26	0.00	0.00	27.27	0.00	0.00	0.00
Hubei mosquito virus 4	TRUE	TRUE	0.00	0.00	0.00	0.00	54.55	0.00	0.00	0.00
Manitoba tombus-like virus 1*	TRUE	TRUE	0.00	0.00	0.00	0.00	45.45	0.00	0.00	0.00
+ssRNA - Tymoviridae
Hubei macula-like virus 3	TRUE	TRUE	0.00	21.05	0.00	0.00	0.00	20.00	0.00	0.00
Manitoba tymo-like virus 1*	FALSE	TRUE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
+ssRNA - Virgaviridae
Hubei virga-like virus 2	TRUE	TRUE	0.00	0.00	0.00	0.00	36.36	0.00	0.00	0.00
Manitoba virgavirus 1*	TRUE	FALSE	0.00	0.00	0.00	0.00	0.00	20.00	0.00	0.00
-ssRNA - Chuviridae
Chuvirus	TRUE	TRUE	0.00	89.47	0.00	0.00	9.09	60.00	0.00	0.00
-ssRNA - Culex rhabdovirus
Culex rhabdovirus	FALSE	TRUE	0.00	0.00	0.00	0.00	18.18	0.00	0.00	0.00
-ssRNA - Flanders hapavirus
Flanders hapavirus	TRUE	TRUE	0.00	15.79	0.00	0.00	90.91	0.00	0.00	0.00
-ssRNA - Orthomyxoviridae
Wuhan mosquito virus 6	TRUE	TRUE	0.00	10.53	0.00	16.67	100.00	0.00	0.00	0.00
Astopletus virus	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
-ssRNA - Peribunyaviridae
Culex bunyavirus 2	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
-ssRNA - Rhabdoviridae
Canya virus	TRUE	TRUE	100.00	0.00	0.00	0.00	90.91	0.00	0.00	0.00
Manitoba rhabdovirus 2*	TRUE	FALSE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Culex Rhabdo-like virus	TRUE	TRUE	0.00	0.00	0.00	0.00	27.27	0.00	0.00	0.00
Elisy virus	TRUE	TRUE	0.00	0.00	0.00	0.00	45.45	0.00	0.00	0.00
Manitoba virus	FALSE	TRUE	0.00	0.00	0.00	0.00	9.09	0.00	0.00	0.00
Merida virus	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
dsDNA - Iridoviridae
Manitoba iridescent virus 1*	FALSE	TRUE	0.00	0.00	0.00	16.67	0.00	0.00	0.00	0.00
dsRNA - Birnaviridae
Ballard Lake virus	TRUE	TRUE	0.00	100.00	0.00	66.67	18.18	20.00	0.00	0.00
dsRNA - Partitiviridae
Partitivirus-like Culex mosquito virus	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
dsRNA - Totiviridae
Manitoba toti-like virus 2*	FALSE	TRUE	100.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
Manitoba toti-like virus 1*	TRUE	TRUE	0.00	10.53	0.00	0.00	27.27	0.00	0.00	0.00
Gouley virus	TRUE	FALSE	0.00	0.00	0.00	0.00	27.27	0.00	0.00	0.00
Snelk virus	TRUE	TRUE	0.00	0.00	0.00	0.00	36.36	0.00	0.00	0.00
Manitoba toti-like virus 3*	TRUE	FALSE	0.00	0.00	0.00	0.00	0.00	80.00	0.00	0.00
Manitoba toti-like virus 4*	TRUE	FALSE	0.00	0.00	0.00	0.00	0.00	0.00	0.00	100.00
ssDNA - Parvoviridae
Aedes vexans densovirus isolate	FALSE	TRUE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Culex densovirus	TRUE	TRUE	0.00	5.26	0.00	66.67	9.09	0.00	0.00	0.00
Aedes albopictus densovirus	FALSE	TRUE	0.00	0.00	0.00	33.33	9.09	0.00	0.00	0.00
MAG: Grus japonensis parvoviridae sp	FALSE	TRUE	0.00	0.00	0.00	16.67	0.00	0.00	0.00	0.00
* Putatively novel virus

Virus Profiles

Below are summaries for each virus detected.

virus_profile_table <- function(virus) {

 virus_table <<-  virus_master_2023 %>% 
  filter(virus_name == virus) %>% 
  #select(-"contig_sequences") %>% 
  summarise(
    num_species = n_distinct(mosquito_species),
    num_contig = n(),
    longest_contig = max(contig_length),
    shortest_contig = min(contig_length),
    avg_nt_id = mean(greatest_identity_percent),
    max_nt_id = max(greatest_identity_percent),
    min_nt_id = min(greatest_identity_percent)
    
  ) %>% 
  gt() %>% 
  cols_label(
    longest_contig = "Max Contig",
    shortest_contig = "Min Contig",
    avg_nt_id = "Average aa Id",
    max_nt_id = "Max aa Id",
    min_nt_id = "Min aa Id",
    num_contig = "n Contigs",
    num_species = "n Species"
  ) %>% 
  tab_header(
    title = paste0("Summary Stats for", " ", virus)
  ) %>% 
    fmt_number(
      columns = 4:last_col(),
      decimals = 2
    )

}

# Arrange df for virus reporting
virus_master_2023 <<- virus_master_2023 %>% 
  mutate(across(.cols = "virus_name",
                ~case_when(grepl("Manitoba", virus_name) & !grepl("Manitoba virus", virus_name) ~ 
                             paste0(., "*"),
                           TRUE ~ .))) %>% 
  arrange(desc(genome)) %>% 
  drop_na(virus_name)

for(virus in unique(virus_master_2023$virus_name)) {

  genome <- virus_master_2023 %>% 
    arrange(desc(genome)) %>% 
    drop_na(virus_name) %>%  
    filter(virus_name == virus) %>% 
    pull(genome) %>% 
    head(1)
  
  genome <- paste0(genome)
  
  family <- virus_master_2023 %>% 
    filter(virus_name == virus) %>% 
    pull(viral_family) %>% 
    head(1)
  
  family <- paste0(family)

  sample_detections <- virus_master_2023 %>% 
    filter(virus_name == virus) %>% 
    distinct(sample_number)
  sample_detections <- paste0(nrow(sample_detections))
  
  
  cat('\n\n#', virus, '\n\n')
  
  cat('\n\n>', virus, 'has a ', genome, 'genome and is a member of the family', family, 'and was detected in', sample_detections, 'sample(s).', 'See summary figures and tables below.',  '\n\n')
  
print(suppressMessages(
  virus_master_2023 %>% 
    filter(virus_name == virus) %>% 
    select(-"contig_sequence") %>% 
    group_by(mosquito_species, collection_year, location_pool) %>% 
    summarise(n = n_distinct(sample_number)) %>% 
    ggplot(aes(x = mosquito_species, y = n, fill = location_pool)) +
    geom_col() +
    facet_grid(. ~ collection_year) +
    scale_fill_viridis_d("Location", option = "magma") +
    theme_bw() +
    labs(title = paste0("Number of Virus Detections"),
       subtitle = paste0("For ", virus, " by Year, Species and Location")) +
    theme(plot.title = element_text(size = 16, face = "bold"),
        axis.title.x = element_blank(),
        axis.text.x = element_text(angle = 45, vjust = 0.5))
  ))
  
  cat('\n\n###', 'Years {.unlisted .unnumbered}', '\n\n')

  print(htmltools::tagList(
    virus_master_2023 %>% 
      filter(virus_name == virus) %>% 
      group_by(collection_year) %>% 
      summarise(n = n_distinct(sample_number)) %>% 
      gt() %>% 
      cols_label(collection_year = "Year(s) Detected")
    ))
  
  cat('\n\n###', 'Locations {.unlisted .unnumbered}', '\n\n')
  
    print(htmltools::tagList(
    virus_master_2023 %>% 
      filter(virus_name == virus) %>% 
      group_by(location_pool) %>% 
      summarise(n = n_distinct(sample_number)) %>% 
      gt() %>% 
      cols_label(location_pool = "Location(s) Detected")
    ))
    
    cat('\n\n###', 'Mosquito Species {.unlisted .unnumbered}', '\n\n')
  
    print(htmltools::tagList(
    virus_master_2023 %>% 
      filter(virus_name == virus) %>% 
      group_by(mosquito_species) %>% 
      summarise(n = n_distinct(sample_number)) %>% 
      gt() %>% 
      cols_label(mosquito_species = "Mosquito Hosts")
    ))
    
    cat('\n\n###', 'Contig Summary {.unlisted .unnumbered}', '\n\n')

  virus_profile_table(virus)
  
  print(htmltools::tagList(virus_table))
  
  cat('\n\n###', 'aa Identity Summary {.unlisted .unnumbered}', '\n\n')
  
  print(suppressMessages(
  virus_master_2023 %>% 
    filter(virus_name == virus) %>% 
    select(-"contig_sequence") %>% 
    ggplot(aes(x = greatest_identity_percent)) +
    geom_histogram(aes(fill = greatest_identity_percent < 90)) +
    geom_vline(xintercept = 90, linetype = "dotted", colour = "firebrick") +
    theme_bw() +
    labs(title = paste0("aa Identity"),
       subtitle = paste0("For ", virus),
       x = "aa Identity", 
       y = "Number of Contigs") +
    theme(plot.title = element_text(size = 16, face = "bold"),
        axis.title.x = element_blank(),
        axis.text.x = element_text(angle = 45, vjust = 0.5)) +
    theme(legend.position = "none")
  ))
  
}

Culex densovirus

Culex densovirus has a ssDNA genome and is a member of the family Parvoviridae and was detected in 6 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	3

Locations

Location(s) Detected	n
Cypress River	3
Cypress River & Carberry	1
Shoal Lake	1
Western MB	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1
Coquillettidia perturbans	4
Culex tarsalis	1

Contig Summary

Summary Stats for Culex densovirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	8	1697	393.00	99.56	100.00	97.71

aa Identity Summary

Aedes albopictus densovirus

Aedes albopictus densovirus has a ssDNA genome and is a member of the family Parvoviridae and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	3

Locations

Location(s) Detected	n
Cypress River	2
Virden	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	2
Culex tarsalis	1

Contig Summary

Summary Stats for Aedes albopictus densovirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	4	3355	323.00	97.46	100.00	89.86

aa Identity Summary

Aedes vexans densovirus isolate

Aedes vexans densovirus isolate has a ssDNA genome and is a member of the family Parvoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Cypress River	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Aedes vexans densovirus isolate
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	3367	3,367.00	100.00	100.00	100.00

aa Identity Summary

MAG: Grus japonensis parvoviridae sp

MAG: Grus japonensis parvoviridae sp has a ssDNA genome and is a member of the family Parvoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Cypress River	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1

Contig Summary

Summary Stats for MAG: Grus japonensis parvoviridae sp
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	570	570.00	100.00	100.00	100.00

aa Identity Summary

Snelk virus

Snelk virus has a dsRNA genome and is a member of the family Totiviridae and was detected in 4 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	1

Locations

Location(s) Detected	n
Brandon	1
Carberry	1
Cypress River & Carberry	1
Shoal Lake, Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	4

Contig Summary

Summary Stats for Snelk virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	4	295	262.00	100.00	100.00	100.00

aa Identity Summary

Partitivirus-like Culex mosquito virus

Partitivirus-like Culex mosquito virus has a dsRNA genome and is a member of the family Partitiviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Partitivirus-like Culex mosquito virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	12	1751	299.00	100.00	100.00	100.00

aa Identity Summary

Gouley virus

Gouley virus has a dsRNA genome and is a member of the family Totiviridae and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3

Locations

Location(s) Detected	n
Brandon	1
Cypress River & Carberry	1
Shoal Lake, Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	3

Contig Summary

Summary Stats for Gouley virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	3	368	263.00	95.04	97.67	92.86

aa Identity Summary

Manitoba toti-like virus 1*

Manitoba toti-like virus 1* has a dsRNA genome and is a member of the family Totiviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	2
2021	3

Locations

Location(s) Detected	n
Brandon	1
Cypress River	1
Shoal Lake	3

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2
Culex tarsalis	3

Contig Summary

Summary Stats for Manitoba toti-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	5	8930	2,012.00	69.92	73.11	67.43

aa Identity Summary

Ballard Lake virus

Ballard Lake virus has a dsRNA genome and is a member of the family Birnaviridae and was detected in 26 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	10
2021	16

Locations

Location(s) Detected	n
Boissevain	2
Brandon	4
Carberry	1
Cypress River	3
Cypress River & Carberry	1
Killarney	2
Newdale	1
Shoal Lake	5
Souris	2
Virden	2
Virden & Souris	1
WPG Insect Contol	2

Mosquito Species

Mosquito Hosts	n
Aedes vexans	19
Coquillettidia perturbans	4
Culex tarsalis	2
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Ballard Lake virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
4	48	3472	707.00	99.86	100.00	93.27

aa Identity Summary

Manitoba toti-like virus 2*

Manitoba toti-like virus 2* has a dsRNA genome and is a member of the family Totiviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1

Contig Summary

Summary Stats for Manitoba toti-like virus 2*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	3123	3,123.00	60.24	60.24	60.24

aa Identity Summary

Manitoba toti-like virus 4*

Manitoba toti-like virus 4* has a dsRNA genome and is a member of the family Totiviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Multiple	1

Mosquito Species

Mosquito Hosts	n
Ochlerotatus triseriatus	1

Contig Summary

Summary Stats for Manitoba toti-like virus 4*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	4909	4,909.00	89.07	89.07	89.07

aa Identity Summary

Manitoba toti-like virus 3*

Manitoba toti-like virus 3* has a dsRNA genome and is a member of the family Totiviridae and was detected in 4 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4

Locations

Location(s) Detected	n
Boissevain & Killarney	1
Brandon	1
Shoal Lake	1
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Ochlerotatus dorsalis	4

Contig Summary

Summary Stats for Manitoba toti-like virus 3*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	4	4626	1,821.00	73.53	74.90	72.22

aa Identity Summary

Manitoba iridescent virus 1*

Manitoba iridescent virus 1* has a dsDNA genome and is a member of the family Iridoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Cypress River	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1

Contig Summary

Summary Stats for Manitoba iridescent virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	797	797.00	78.74	78.74	78.74

aa Identity Summary

Chuvirus

Chuvirus has a -ssRNA genome and is a member of the family Chuviridae and was detected in 21 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	9
2021	12

Locations

Location(s) Detected	n
Boissevain	2
Boissevain & Killarney	1
Brandon	3
Carberry	2
Cypress River	1
Cypress River & Carberry	1
Killarney	1
Newdale	1
Shoal Lake	6
Souris	1
Virden	1
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	17
Culex tarsalis	1
Ochlerotatus dorsalis	3

Contig Summary

Summary Stats for Chuvirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	39	6799	433.00	97.49	100.00	89.66

aa Identity Summary

Merida virus

Merida virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Merida virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	55	7483	262.00	99.86	100.00	97.14

aa Identity Summary

Wuhan mosquito virus 6

Wuhan mosquito virus 6 has a -ssRNA genome and is a member of the family Orthomyxoviridae and was detected in 14 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	7
2021	7

Locations

Location(s) Detected	n
Boissevain	1
Brandon	4
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	2
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1
Western MB	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2
Coquillettidia perturbans	1
Culex tarsalis	11

Contig Summary

Summary Stats for Wuhan mosquito virus 6
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	101	2467	252.00	99.76	100.00	97.69

aa Identity Summary

Canya virus

Canya virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4
2021	7

Locations

Location(s) Detected	n
Boissevain	1
Brandon	4
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1
Culex tarsalis	10

Contig Summary

Summary Stats for Canya virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	14	6071	522.00	87.32	100.00	66.04

aa Identity Summary

Flanders hapavirus

Flanders hapavirus has a -ssRNA genome and is a member of the family Flanders hapavirus and was detected in 13 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	8

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	3
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3
Culex tarsalis	10

Contig Summary

Summary Stats for Flanders hapavirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	81	8773	263.00	99.90	100.00	95.96

aa Identity Summary

Astopletus virus

Astopletus virus has a -ssRNA genome and is a member of the family Orthomyxoviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Astopletus virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	29	1044	464.00	99.06	100.00	95.77

aa Identity Summary

Elisy virus

Elisy virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	2

Locations

Location(s) Detected	n
Brandon	3
Cypress River & Carberry	1
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	5

Contig Summary

Summary Stats for Elisy virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	21	1817	373.00	99.27	100.00	96.41

aa Identity Summary

Culex Rhabdo-like virus

Culex Rhabdo-like virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1
2021	2

Locations

Location(s) Detected	n
Brandon	1
Cypress River & Carberry	1
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	3

Contig Summary

Summary Stats for Culex Rhabdo-like virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	4	1973	672.00	100.00	100.00	100.00

aa Identity Summary

Culex bunyavirus 2

Culex bunyavirus 2 has a -ssRNA genome and is a member of the family Peribunyaviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Culex bunyavirus 2
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	19	1896	350.00	100.00	100.00	100.00

aa Identity Summary

Manitoba virus

Manitoba virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	1

Contig Summary

Summary Stats for Manitoba virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	5	1589	500.00	99.76	100.00	98.80

aa Identity Summary

Culex rhabdovirus

Culex rhabdovirus has a -ssRNA genome and is a member of the family Culex rhabdovirus and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	2

Locations

Location(s) Detected	n
Brandon	1
Cypress River	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	2

Contig Summary

Summary Stats for Culex rhabdovirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	429	359.00	100.00	100.00	100.00

aa Identity Summary

Manitoba rhabdovirus 2*

Manitoba rhabdovirus 2* has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Manitoba rhabdovirus 2*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	4648	4,648.00	75.00	75.00	75.00

aa Identity Summary

Manitoba picorna-like virus 1*

Manitoba picorna-like virus 1* has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 22 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	11
2021	11

Locations

Location(s) Detected	n
Boissevain	2
Boissevain & Killarney	1
Brandon	4
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Killarney	2
Newdale	1
Shoal Lake	5
Souris	1
Virden	1
Virden & Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	19
Ochlerotatus dorsalis	3

Contig Summary

Summary Stats for Manitoba picorna-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	86	4085	510.00	87.73	100.00	73.93

aa Identity Summary

Manitoba Rhabdovirus 1*

Manitoba Rhabdovirus 1* has a +ssRNA genome and is a member of the family Rhabdoviridae and was detected in 20 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	9
2021	11

Locations

Location(s) Detected	n
Boissevain	2
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Killarney	2
Newdale	1
Shoal Lake	5
Souris	1
Virden	1
Virden & Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	19
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Manitoba Rhabdovirus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	37	8033	718.00	83.22	93.01	69.42

aa Identity Summary

Hanko iflavirus 1

Hanko iflavirus 1 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 12 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	8
2021	4

Locations

Location(s) Detected	n
Boissevain & Killarney	1
Brandon	1
Cypress River	1
Newdale	1
Shoal Lake	4
Virden & Souris	1
WPG Insect Contol	3

Mosquito Species

Mosquito Hosts	n
Aedes vexans	4
Coquillettidia perturbans	1
Culex tarsalis	1
Ochlerotatus dorsalis	5
Ochlerotatus flavescens	1

Contig Summary

Summary Stats for Hanko iflavirus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
5	30	9246	308.00	97.49	100.00	93.45

aa Identity Summary

Manitoba iflavirus 1*

Manitoba iflavirus 1* has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 17 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	16
2021	1

Locations

Location(s) Detected	n
Boissevain & Killarney	1
Brandon	5
Cypress River & Carberry	2
Killarney	1
Shoal Lake	4
Virden & Souris	1
WPG Insect Contol	2
Western MB	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	7
Coquillettidia perturbans	2
Culex tarsalis	3
Ochlerotatus dorsalis	4
Ochlerotatus flavescens	1

Contig Summary

Summary Stats for Manitoba iflavirus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
5	25	9899	286.00	93.47	100.00	89.14

aa Identity Summary

Marma virus

Marma virus has a +ssRNA genome and is a member of the family Luteoviridae and was detected in 12 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	6
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1
Western MB	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1
Culex tarsalis	11

Contig Summary

Summary Stats for Marma virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	23	3160	1,574.00	100.00	100.00	100.00

aa Identity Summary

Culex iflavilike virus 3

Culex iflavilike virus 3 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Culex iflavilike virus 3
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	183	1824	250.00	99.49	100.00	94.19

aa Identity Summary

Placeda virus

Placeda virus has a +ssRNA genome and is a member of the family Flaviviridae and was detected in 13 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	6
2021	7

Locations

Location(s) Detected	n
Boissevain	1
Brandon	4
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	2
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2
Culex tarsalis	11

Contig Summary

Summary Stats for Placeda virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	169	11737	252.00	97.87	100.00	86.24

aa Identity Summary

Culex Iflavi-like virus 4

Culex Iflavi-like virus 4 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 7 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4
2021	3

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River & Carberry	1
Shoal Lake, Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	7

Contig Summary

Summary Stats for Culex Iflavi-like virus 4
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	23	9811	285.00	99.81	100.00	96.20

aa Identity Summary

Hubei mosquito virus 4

Hubei mosquito virus 4 has a +ssRNA genome and is a member of the family Tombusviridae and was detected in 6 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	3

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River & Carberry	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	6

Contig Summary

Summary Stats for Hubei mosquito virus 4
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	6	5103	367.00	96.50	100.00	92.65

aa Identity Summary

Hubei virga-like virus 2

Hubei virga-like virus 2 has a +ssRNA genome and is a member of the family Virgaviridae and was detected in 4 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	1

Locations

Location(s) Detected	n
Brandon	2
Cypress River & Carberry	1
Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	4

Contig Summary

Summary Stats for Hubei virga-like virus 2
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	6	947	290.00	99.04	100.00	96.27

aa Identity Summary

Des Moines River virus

Des Moines River virus has a +ssRNA genome and is a member of the family Tombusviridae and was detected in 4 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4

Locations

Location(s) Detected	n
Brandon	3
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1
Culex tarsalis	3

Contig Summary

Summary Stats for Des Moines River virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	4	2361	1,070.00	100.00	100.00	100.00

aa Identity Summary

Manitoba dicistro-like virus 1*

Manitoba dicistro-like virus 1* has a +ssRNA genome and is a member of the family Dicistroviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	1

Contig Summary

Summary Stats for Manitoba dicistro-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	7146	7,146.00	82.61	82.61	82.61

aa Identity Summary

Soybean thrips dicistrovirus

Soybean thrips dicistrovirus has a +ssRNA genome and is a member of the family Dicistroviridae and was detected in 9 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	6

Locations

Location(s) Detected	n
Boissevain	2
Brandon	1
Carberry	1
Newdale	1
Shoal Lake	2
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3
Culex tarsalis	5
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Soybean thrips dicistrovirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	11	9121	893.00	100.00	100.00	100.00

aa Identity Summary

Yongsan picorna-like virus 2

Yongsan picorna-like virus 2 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1
2021	2

Locations

Location(s) Detected	n
Brandon	2
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	3

Contig Summary

Summary Stats for Yongsan picorna-like virus 2
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	4	9573	2,367.00	100.00	100.00	100.00

aa Identity Summary

Manitoba tombus-like virus 1*

Manitoba tombus-like virus 1* has a +ssRNA genome and is a member of the family Tombusviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	2

Locations

Location(s) Detected	n
Brandon	2
Shoal Lake	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	5

Contig Summary

Summary Stats for Manitoba tombus-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	6	2351	1,687.00	79.73	100.00	72.73

aa Identity Summary

Culex narnavirus 1

Culex narnavirus 1 has a +ssRNA genome and is a member of the family Narnaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	1

Contig Summary

Summary Stats for Culex narnavirus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	513	513.00	100.00	100.00	100.00

aa Identity Summary

Hubei noda-like virus 12

Hubei noda-like virus 12 has a +ssRNA genome and is a member of the family Nodaviridae and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	2

Locations

Location(s) Detected	n
Carberry	1
Virden	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1
Culex tarsalis	1

Contig Summary

Summary Stats for Hubei noda-like virus 12
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	2	4762	841.00	95.83	100.00	91.67

aa Identity Summary

Manitoba mononega-like virus 1*

Manitoba mononega-like virus 1* has a +ssRNA genome and is a member of the family Negevirus and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1
2021	1

Locations

Location(s) Detected	n
Brandon	1
Multiple	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1
Ochlerotatus triseriatus	1

Contig Summary

Summary Stats for Manitoba mononega-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	3	11375	5,456.00	80.60	90.00	73.21

aa Identity Summary

Serbia mononega-like virus 1

Serbia mononega-like virus 1 has a +ssRNA genome and is a member of the family Negevirus and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1

Contig Summary

Summary Stats for Serbia mononega-like virus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	2477	2,477.00	75.00	75.00	75.00

aa Identity Summary

Hubei macula-like virus 3

Hubei macula-like virus 3 has a +ssRNA genome and is a member of the family Tymoviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4
2021	1

Locations

Location(s) Detected	n
Brandon	2
Shoal Lake	2
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	4
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Hubei macula-like virus 3
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	8	6059	2,954.00	96.13	100.00	92.15

aa Identity Summary

Hanko iflavirus 2

Hanko iflavirus 2 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 18 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	11
2021	7

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Cypress River & Carberry	1
Killarney	2
Newdale	1
Shoal Lake	5
Souris	1
Virden	1
Virden & Souris	1
WPG Insect Contol	2

Mosquito Species

Mosquito Hosts	n
Aedes vexans	15
Coquillettidia perturbans	1
Ochlerotatus dorsalis	2

Contig Summary

Summary Stats for Hanko iflavirus 2
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	29	9206	461.00	88.70	100.00	67.08

aa Identity Summary

Black queen cell virus

Black queen cell virus has a +ssRNA genome and is a member of the family Dicistroviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Black queen cell virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	6035	2,087.00	100.00	100.00	100.00

aa Identity Summary

Cordoba virus

Cordoba virus has a +ssRNA genome and is a member of the family Negevirus and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	3

Locations

Location(s) Detected	n
Boissevain	1
Cypress River	1
Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3

Contig Summary

Summary Stats for Cordoba virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	14	5133	610.00	97.10	100.00	93.75

aa Identity Summary

Mekrijarvi Negevirus

Mekrijarvi Negevirus has a +ssRNA genome and is a member of the family Negevirus and was detected in 6 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	2
2021	4

Locations

Location(s) Detected	n
Boissevain	1
Boissevain & Killarney	1
Cypress River	1
Shoal Lake	1
Souris	1
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3
Ochlerotatus dorsalis	3

Contig Summary

Summary Stats for Mekrijarvi Negevirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	6	9873	3,125.00	94.13	100.00	90.78

aa Identity Summary

Manitoba mononega-like virus 2*

Manitoba mononega-like virus 2* has a +ssRNA genome and is a member of the family Negevirus and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1
2021	2

Locations

Location(s) Detected	n
Boissevain	1
Brandon	1
Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3

Contig Summary

Summary Stats for Manitoba mononega-like virus 2*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	3	9570	2,735.00	98.77	100.00	96.30

aa Identity Summary

Hubei arthropod virus 1

Hubei arthropod virus 1 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Hubei arthropod virus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	2967	2,967.00	100.00	100.00	100.00

aa Identity Summary

Soybean thrips iflavirus 4

Soybean thrips iflavirus 4 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1

Contig Summary

Summary Stats for Soybean thrips iflavirus 4
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	3835	3,835.00	100.00	100.00	100.00

aa Identity Summary

Cafluga virus

Cafluga virus has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	2

Locations

Location(s) Detected	n
Boissevain & Killarney	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Cafluga virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	2	3426	1,395.00	99.77	100.00	99.55

aa Identity Summary

Manitoba tymo-like virus 1*

Manitoba tymo-like virus 1* has a +ssRNA genome and is a member of the family Tymoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Boissevain	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Manitoba tymo-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	6302	6,302.00	66.79	66.79	66.79

aa Identity Summary

Utsjoki negevirus 3

Utsjoki negevirus 3 has a +ssRNA genome and is a member of the family Negevirus and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	2

Locations

Location(s) Detected	n
Shoal Lake	1
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2

Contig Summary

Summary Stats for Utsjoki negevirus 3
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	989	972.00	99.02	99.03	99.01

aa Identity Summary

Inari jingmenvirus

Inari jingmenvirus has a +ssRNA genome and is a member of the family Flaviviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Inari jingmenvirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	1267	1,267.00	100.00	100.00	100.00

aa Identity Summary

Manitoba virgavirus 1*

Manitoba virgavirus 1* has a +ssRNA genome and is a member of the family Virgaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Manitoba virgavirus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	1675	1,675.00	83.83	83.83	83.83

aa Identity Summary

Manitoba narnavirus 1*

Manitoba narnavirus 1* has a +ssRNA genome and is a member of the family Narnaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Anopheles earlei	1

Contig Summary

Summary Stats for Manitoba narnavirus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	1760	654.00	80.59	80.89	80.29

aa Identity Summary